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With normal mappers like the price one, we have no issues in replacing values, but the product reference one is slightly different because it relates the node (display) with the product id from commerce_product in a sepparate field.
If you want to load product references, the first time is just fine, but for updates you need to send all the product references again for adding a new one, which in some cases could be a pain.
Maybe it would make sense to have two mappers, one that is quicker and straightforward, replaces the field contents and that's it, another one would be "acumulative", and would not delete product ids but add them to the reference field.
I have a proof of concept working, if it makes sense I'll post the code here.